Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::Tools::Genomewise - Results of one Genomewise run


         use Bio::Tools::Genomewise;
         my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out");

         while (my $gene = $gw->next_prediction){
             my @transcripts = $gene->transcripts;
             foreach my $t(@transcripts){
               my @exons =  $t->exons;
               foreach my $e(@exons){
                   print $e->start." ".$e->end."\n";


       This is the parser for the output of Genewise. It takes either a file handle or a file
       name and returns a Bio::SeqFeature::Gene::GeneStructure object.  You will need to specify
       the proper target sequence id on the object with the $feature->seq_id($seqid).


   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

AUTHOR - Fugu Team, Jason Stajich



       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : $obj->new(-file=>"genewise.out");
        Function: Constructor for genomewise wrapper. Takes either a file or filehandle
        Example :
        Returns : L<Bio::Tools::Genomewise>

        Title   : _get_strand
        Usage   : $obj->_get_strand
        Function: takes start and end values, swap them if start>end and returns end
        Example :
        Returns :$start,$end,$strand

        Title   : score
        Usage   : $obj->score
        Function: get/set for score info
        Example :
        Returns : a score value

        Title   : _prot_id
        Usage   : $obj->_prot_id
        Function: get/set for protein id
        Example :
        Returns :a protein id

        Title   : _target_id
        Usage   : $obj->_target_id
        Function: get/set for genomic sequence id
        Example :
        Returns :a target id

        Title   : next_prediction
        Usage   : while($gene = $genewise->next_prediction()) {
                         # do something
        Function: Returns the gene structure prediction of the Genomewise result
                  file. Call this method repeatedly until FALSE is returned.

        Example :
        Returns : a Bio::SeqFeature::Gene::GeneStructure object
        Args    :